libSBML Python API  5.10.0
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convertLayout.py

Converts SBML Layout and Render datra from SBML Level 2 to Level 3 and vice versa.

1 #!/usr/bin/env python
2 ##
3 ## @file convertLayout.py
4 ## @author Frank T. Bergmann
5 ##
6 ## <!--------------------------------------------------------------------------
7 ## This sample program is distributed under a different license than the rest
8 ## of libSBML. This program uses the open-source MIT license, as follows:
9 ##
10 ## Copyright (c) 2013-2014 by the California Institute of Technology
11 ## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
12 ## and the University of Heidelberg (Germany), with support from the National
13 ## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
14 ##
15 ## Permission is hereby granted, free of charge, to any person obtaining a
16 ## copy of this software and associated documentation files (the "Software"),
17 ## to deal in the Software without restriction, including without limitation
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19 ## and/or sell copies of the Software, and to permit persons to whom the
20 ## Software is furnished to do so, subject to the following conditions:
21 ##
22 ## The above copyright notice and this permission notice shall be included in
23 ## all copies or substantial portions of the Software.
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32 ##
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34 ## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
35 ## of Heidelberg, nor the names of any contributors, may be used to endorse
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38 ## ------------------------------------------------------------------------ -->
39 
40 from libsbml import *
41 doc = readSBMLFromFile('D:/DropboxSBML/Dropbox/Bug1867-l3.xml')
42 layoutNsUri = "http://projects.eml.org/bcb/sbml/level2"
43 layoutNs = LayoutPkgNamespaces(2, 4)
44 renderNsUri = "http://projects.eml.org/bcb/sbml/render/level2"
45 renderNs = RenderPkgNamespaces(2, 4)
46 
47 prop = ConversionProperties(SBMLNamespaces(2,4))
48 prop.addOption('strict', False)
49 prop.addOption('setLevelAndVersion', True)
50 prop.addOption('ignorePackages', True)
51 doc.convert(prop)
52 
53 
54 docPlugin = doc.getPlugin("layout")
55 if docPlugin != None:
56  docPlugin.setElementNamespace(layoutNsUri)
57 
58 doc.getSBMLNamespaces().removePackageNamespace(3, 1, "layout", 1);
59 doc.getSBMLNamespaces().addPackageNamespace("layout", 1);
60 
61 rdocPlugin = doc.getPlugin("render");
62 if rdocPlugin!= None:
63  rdocPlugin->setElementNamespace(renderNsUri);
64 
65 doc.getSBMLNamespaces().removePackageNamespace(3, 1, "render", 1);
66 doc.getSBMLNamespaces().addPackageNamespace("render", 1);
67 
68 print doc.toSBML()
69